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I'm confused about the terminology and directions described in processing DNA to proteins in this paragraph.

RNA polymerase reads a DNA template in the 3’ to 5’ direction to synthesize RNA in the 5’ to 3’ direction. Transcription can occur in either direction, but not in either direction from a single promoter. RNA polymerase can only transcribe in one direction (5’ to 3’) with respect to reading one strand of the template DNA in the opposite direction (3’ to 5’). In general, each promoter recruits RNA polymerase to a particular site and indicates in which the direction RNA polymerase will move along the DNA. As RNA polymerase is moving, there will be only a single strand that can be used as a template to allow 5' to 3' synthesis of a transcript.

Sentence 1:

What's the difference between reading and synthesizing RNA?

Sentence 2:

What's the difference between synthesizing and transcribing?

Sentence 3:

Didn't this just contradict sentence 2?

Sentence 4:

If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).

Sentence 5:

My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?

Question:

I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?

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    $\begingroup$ I think if you search youtube for "rna transcription animation" you will find plenty of visual demonstrations. $\endgroup$
    – Superbest
    Commented Feb 4, 2018 at 6:11

2 Answers 2

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What's the difference between reading and synthesizing RNA?

What's the difference between reading and writing a book? Synthesizing RNA means producing an RNA based on a sequence in DNA. Reading it means processing RNA that is already produced. Reading also implies that protein will be produced based on the sequence in RNA.

What's the difference between synthesizing and transcribing?

"Synthesize" means to produce any chemical molecule. "Transcribe" is specifically the synthesis of RNA form DNA via a polymerase (as opposed to for instance inorganic synthesis of RNA de novo, as might be done in a chemistry lab).

Didn't this just contradict sentence 2?

It's just saying that genes can be oriented forward or in reverse. Reverse genes are on the opposite strand, so they are still 5' to 3' (the 5' ends of the two strands are on opposite ends of the DNA). But every gene must still have a promoter on its 5' side.

And actually, that bit is not quite true: There are bidirectional promoters that will cause transcription in both directions.

If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).

Usually, it will transcribe (so it will also synthesize, or "read"). But technically, RNA pols belong to a family of proteins which are "molecular motors", meaning that their fundamental activity is to move along DNA step by step like a little monkey climbing a ladder. With RNA pols, RNA synthesis is coupled to this movement, so each step on DNA also causes a letter to be added to the RNA they are making.

Also, technically the RNA pol is not only moving and making DNA, but also unwinding the two strands of DNA and separating them. But this may be outside the scope of your material.

My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?

RNA comes out matching the sequence of the gene (except for T->U), and it is assembled through basepairing to DNA. If it paired with the strand the gene is on, the RNA would come out as the reverse complement of the gene. Instead it is assembled on the opposite strand, which is already the RC of the gene. RC of RC of a sequence is the same sequence. Thus we say RNA is transcribed from the "non-coding" strand, but keep in mind that these coding/non-coding assignments are arbitrary and only used by us humans, the cell does not have a special marking for it (beyond the 5'/3').

I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?

It's very simple: DNA is a directed (because of 5'/3') string of ACTG. It is coupled to another, complementary string that runs opposite to it. The sequence on either strand may be meaningless, or parts of it may encode genes. Genes consist of a promoter, some sequence, and terminator. RNA pols can slide along either strand, but only in 5' to 3' direction, so they will slide in opposite directions on opposite strands, like cars on a two way street. When RNA pol encounters a promoter, it starts synthesizing an RNA: It separates the two strands, and lets single RNTPs basepair with the opposite-direction strand, when they do so it glues their phosphate backbones together. It keeps sliding and making RNA like this until it reaches another sequence, the terminator, at which point it stops assembling RNA and releases it. The RNA snaps off DNA and goes off on its merry way, the two strands of the DNA that were separated by RNA pol come together again.

Thus for every promoter-terminator pair, whatever sequence is in between them will be transcribed into an RNA. These are basically genes. These genes may be on either strand of DNA, and they must always be oriented along the 5' to 3' of the strand they are on. Thus genes on opposite strands will appear "reversed" with respect to each other.

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"Sentence 1:

What's the difference between reading and synthesizing RNA?"

Sentence 1 relates to what is the most trivial if most important to not mis-understand: RNA polymerase is said to "work" ( Wikipedia, RNA polymerase) in 5' to 3' direction.

In order to paraphrase your question accordingly: What would "to work" mean in that sentence? It would mean "synthesizing" RNA, it would not mean "reading" DNA (the reading I circumscribe as "unraveling/traveling" from '3 to '5, while, at the same time, "elongating" in '5 to '3 direction). As it now occurs: The text says "... RNA polymerase reads a DNA template..."! Thus, changing your question to "...difference between reading DNA (do not omit "DNA") and synthesizing RNA apparently answers the question. However, that is not the whole story. I think it doesn't come easy to see that, see above, the "work" is like old fashioned homework (in German: "Stricken"): What you have just seen is what you got to add - to the end (to paraphrase some common acronym).

If polymerase had some bench or large table it'd go "a-head" and work from 5 to 3, not the other way round. Polymerase must put the letter that it had just read as been ordered to the end of the list that "goes out", that polymerase thus "table-waited" from 5 to 3, which makes "sense". So - "reading" might very well be "synthesizing" in terms of direction - however, defined by mechanism, it is not (it is first in, DNA, first out, RNA, "nothing in store"). Again, in some surprising way - to be specific: in terms of direction - reading could be, but is not synthesizing.

"Sentence 2:

What's the difference between synthesizing and transcribing?"

Sentence 2 does not use the word transcribing. In the context of sentence 2 synthesing and transcribing are synonymous.

"Sentence 3:

Didn't this just contradict sentence 2?"

Sentence 3 does not preliminarily explain what sentence 4, the following, explains: "...each promoter ... indicates in which the direction RNA polymerase will move along the DNA." Thus sentence 3 does not seem to "clear up" the ambiguity of sentence 2 which lies in the issue of "direction". The word "direction" in sentence two does not make clear how "direction" relates to the concept of direction as the author makes use of in sentence 1. One specific gene defines "any" direction (which you wrote about in some answer of yours).*

"Sentence 4:

If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?)."

It transcribes (most general term) by reading (the template/anti-sense) DNA and synthesizing RNA (cp. answer on sentence 1 above) accordingly, first in first out, elongating first becomes last (there is no memory).

"Sentence 5:

My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?"

Correct.

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